Canonical URLs affecting Google Cache

I am using canonical URLS because I installed WP on its own directory

Do you mean custom permalinks? Or have you added some of your own redirects?

Have you created and submitted a Google XML sitemap?

hi.. this is what I mean:

https://www.mysite.com

and

https://www.mysite.com/wordpress

the URLs to all of my pages and posts have this configuration:
https://www.mysite.com/wordpress/post-title.hml

each time i check the google cache for https://www.mysite.com is different to that of https://www.mysite.com/wordpress.

yes, i have been using google sitemaps for over a year now… i set it up to see the sitemap on the root directory, not on the WP directory…

Have you looked at the sitemap.xml file? Normally Google assumes that the urls within the sitemap are the ones you want used and will ignore the sub-directory ones. Or at least that’s how I understood it last time I checked into this.